In RajLabMSSM/catalogueR: QTL data extraction and colocalization

pkg <- read.dcf("DESCRIPTION", fields = "Package")[1]
description <- read.dcf("DESCRIPTION", fields = "Description")[1]

r pkg: r gsub("echoverse module: ","", description)

This R package is part of the echoverse suite that supports echolocatoR: an automated genomic fine-mapping pipeline.

If you use r pkg, please cite:

r citation(pkg)$textVersion

and

N Kerimov, JD Hayhurst, K Peikova, et al. A compendium of uniformly processed human gene expression and splicing quantitative trait loci. Nat Genet 53, 1290–1299 (2021). https://doi.org/10.1038/s41588-021-00924-w

Installation

if(!require("remotes")) install.packages("remotes")

remotes::install_github("RajLabMSSM/`r pkg`")
library(`r pkg`)

Documentation

Website

Getting started

Notes

• The functions in catalogueR are partly derived from the eQTL Catalogue tutorial.

• The ALT allele is always the effect allele in eQTL Catalogue.

• Additional eQTL Catalogue resources:

• GitHub repository
• In-depth API documentation
• FTP server: ftp://ftp.ebi.ac.uk/pub/databases/spot/eQTL/csv

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Contact

Brian M. Schilder, Bioinformatician II
Raj Lab
Department of Neuroscience, Icahn School of Medicine at Mount Sinai

RajLabMSSM/catalogueR documentation built on Jan. 1, 2023, 10:45 a.m.